That's frustrating Chig! Your body just went through a lot though, and it makes sense to me that it will take a little bit of time for things to get back to normal. Is the length of your cycle somewhat back to normal? I found that my cycles actually stabilized after metho, but I began spotting a few days before AF which had never happened before. I actually don't know that some spotting before AF is anything to really worry about although I do understand wanting things to be as before.
I did not count my spotting days as CD1 and considered it to be the first day of flow when I needed a tampon or a pad versus a panty liner.
Before I got pregnant, my cycles were about 29 days. My periods usually started out with spotting to light bleeding on the first day and then the "flow" would be the heaviest on my second and third days before it would start to taper off by day 6. Now, I am starting out with redish to brownish spotting for 3 days before the "flow" starts.
I am still spotting today, but it is a little heavier spotting, but the weird thing is that my temp went even higher today.

If I don't count these 3 days of spotting as a part my new cycle, then I would be on day 31 of my previous cycle.
So, I am not quite sure what to think of my cycles yet.